- ChimeraX-users - RBVI Mailing Lists

Removing text labels generated with command distance
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script, to be executed in nogui mode, which does the following: -open a pdb file -define centroids for specific residues -draw pseudobonds between specific residues -> I am using the command distance for this purpose The issue arises when I have to save the session (.cxs) when in nogui mode, I am getting this error: QGuiApplication::font(): no QGuiApplication instance and no application font set. I believe it is because of the text labels created by the command distance. So, I included the following in my code: run(session, ‘hide #2.*’) and I can now save the session. I noticed in the model panel that the pdb file is assigned to #1 and the pseudobond to #2. The text labels are created as a submodel of the pseudobond (so #2.1, 2.2,..), hence why the ‘hide #2.*’ Will this fix always work? Is the model assignment also dependent on the pdb file being opened? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

4 4

Where is the renumber sequence tool in ChimeraX?
by Phan, Isabelle 16 May '22

16 May '22

The sequence of my structure includes a tag and I want to renumber from -7 so that the first residue is the start Met. I tried the old chimera command resrenumber = FAIL. I googled and searched the docs, read the list of commands one by one, and still could not figure it out. The API has a renumber_sequence() function but I don't understand the description (what’s "the given residues”? The chain?) and was unable to find an example on how to call this from the interface. I opened the python shell and typed: from chimerax.core.commands import run run(renumber_residues('#1/A:*', -7)) # FAIL Sorry if this is trivial, I am still completely baffled by ChimeraX despite using it for years. Thanks, Isabelle CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 5

align 400 copies of the same density map into a circle
by SHIQING LIAO 16 May '22

16 May '22

Hi there, I am a new user and would really appreciate any input on the task I want to do using Chimerax. Currently I have a mrc map, and it is a part of a cylindrical tube-shaped structure (like the area I drew in the picture). The map looks like a curved plane from the side of the cylinder, if it helps. If I piece 400 identical copies of map with some rotation and transition, I would ideally get a cynlider shaped strutcure, without top and bottom (like the picture below). The reason why I want to piece the mrc together is that I don't have the full look of the tube, but I know the rough radius (that's how 400 was derived), and I want to make a model for the full tube, using the model of the composing protein. I managed to manually fit the models of individual protein into one map. For the other mrc copies, I tried to do the same again but it took a lot of time and not very accurate, so I'm looking for any coding solutions that might help. I'm currently thinking if it is possible for me to place a marker at the center of one mrc map. Then make 400 copies of the map with the marker. Then write a code to tell each 1/400 mrc map to rotate 0.9 degrees around the marked center and move to a coordinate. Then I can repeat the same for the protein models I mapped to one mrc map. But I have no idea how to achieve it, and any suggestions would be greatly appreciated! Thank you so much for helping me!!! Best, Shiqing [image: cf23fde5-632f-4568-9700-9307f24e0f6c.png]

2 1

crossfade issue
by Omid Haji-Ghassemi 16 May '22

16 May '22

Dear ChimeraX community, I am having some issues with the crossfade command while making a movie. For some reason the command stretches out the image while running the transition. I am just doing a simple transition for a movie as part of a more complicated movie. To illustrate the problem I made a simple script that reproduces the issue. movie record supersample 3 size 640,480 wait 60 crossfade; cartoon hide #1/D-F; wait 60 movie encode framerate 60 output test.mov Be great if someone can let me know what I am doing wrong. Best, Omid --------------------------------------------------- --------------------------------------------------- Dr. Omid Haji-Ghassemi Assistant Professor, Biological Sciences Department University of Calgary https://hajighassemilab.org

3 4

Re: [chimerax-users] [Chimera-users] Making a movie from map series while keeping map's colors
by Elaine Meng 16 May '22

16 May '22

Hi Michal, Since this is a ChimeraX question I'm putting it on chimerax-users(a)cgl.ucsf.edu -- otherwise the Chimera users will be confused! In the future you may want to use that address for ChimeraX questions. If I remember correctly, "vseries" re-renders the surfaces at the time of playback, unless you specify storing more of them with the "cacheFrames" option -- so try using "vseries" with "cacheFrames 20": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> See previous answer to a similar question: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003271.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 16, 2022, at 12:45 AM, Michal Arie Shmuelov via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi everyone, > I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. > I’m coloring the map series using the command “color zone #X near #X distance X” (coloring the map according to pdb model). > Next I’m trying to make a movie of this map series while retaining the map colors. > For some reason when the morph/ vseries starts to run the colors disappear. > Can someone help me to solve this problem? > What are the commands that I should write? > Thanks, > Michal >

2 1

Python code for obtaining chain information
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script in which I need generate a list of all the chains present in a structure: e.g [A,B] However, I do not know which module to import in order to write a code for this. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

Showing Bond/PBond to Cartoon/Ribbons
by Anderson, Jacob 13 May '22

13 May '22

There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior). How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon? Good Example - connected to ribbon [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881] Two floating examples: [cid:46516984-036d-4a39-9713-9056a161548a]

3 6

no gui mode and redirecting output of some commands
by Shubham Devesh Ramgoolam 12 May '22

12 May '22

Hi, I hope you are doing well. I have a python script (myscript.py) as follows: from chimerax.core.commands import run import os os.chdir("C:\\Users\\Shubham\\Desktop") run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") # location of my pdb file run(session, "sel aromatic & protein") run(session, "log clear") run (session, "info residue sel") run(session, "log save aromatic_list.html") I am using the following prompt for calling chimerax from command prompt: Gui enabled: chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py Gui disabled: chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py With gui mode enabled, the html file, aromatic_list.html, is created. However, when disabling gui, nothing is created. I suspect this is because I am relying on the log which may not be functional when gui is disabled? Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui? I tried with sys.stdout but it did not work (empty text files were created.). Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 6

interface plot
by Pranav Shah 12 May '22

12 May '22

<3 <3 <3 <3 <3 Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 1

Cartoon “Highlight color” and “Suppress false” Feature
by Gupta, Arun 12 May '22

12 May '22

Hello ChimeraX team, I am just wondering whether the “Pymol Cartoon highlight color” feature of helix and strand has been brought in the newer or the daily build versions of the ChimeraX. Someone has been just recently verbally referring to me that this feature has been updated in the newer versions of ChimeraX, but I couldn’t locate the mention in the ChimeraX mailing list. Also, I have noticed that “cartoon suppress false” command doesn’t work for the NMR ensemble PDBs I think it's more to do with specifying the “cartoon suppress false” command for the individual PDB model within ensemble PDBs. I did try to play around with selection notation for individual model with “cartoon suppress false” command but couldn’t get it right. Can you please specify the exact command notation to work around with NMR ensemble PDBs Thanks! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

2 3

Model number of geometric objects(axes, planes)
by Shubham Devesh Ramgoolam 11 May '22

11 May '22

Hi, I hope you are doing well. I am writing a python script to do the following: 1. Define planes and axes 2. Measure the angle between specific planes and between specific plane and axis The issue I am facing is that I need the model number of these geometric objects when using the command angle. Is there a command that will give the model number of the geometric objects? (In chimera, I would assign a number to the geometric objects when defining them and I would refer to it in the command angle. In chimeraX, I could assign a name to the geometric object but the command angle accept only model number for axes and planes.) Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 2

Re: [chimerax-users] [Chimera-users] Get rotation between two views?
by Elaine Meng 11 May '22

11 May '22

Hi Oliver, Not exactly -- the closest thing I can think of is ChimeraX command "view matrix" but then you'd have to figure it out by comparing the camera matrices given for the two views, if that's even possible. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> When I make figures that differ by N-degree rotation I have to just save one view, then use a command to make that exact rotation, and then save another view before saving the session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 8:50 AM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > In either Chimera or X, is there a way to obtain the orientational relationship between two views? > > E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? > > Cheers > Oli

3 2

select atoms nearest to chain
by Pranav Shah 10 May '22

10 May '22

Hi Elaine, How does one select atoms on one chain that are close to another chain based on a distance cut off? for eg: chain A and B form an interface. I now want to know which residues on chain A fall within a distance of 4Å from chain B and vice versa. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 2

AlphaFold colouring of models predicted outside of ChimeraX
by James Hodgkinson-Bean 10 May '22

10 May '22

Hi Recently I’ve been performing batch AlphaFold predictions on colab. I was wondering if it’s possible to apply the confidence colour pallete to these structures in chimera if they have not been predicted in ChimeraX directly? Thanks, James.

2 2

exporting crosslinks histogram
by Pim Huis in 't Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15- --- Pim J. Huis in ’t Veld, PhD Postdoctoral researcher in the lab of Andrea Musacchio Dept. of Mechanistic Cell Biology Max Planck Institute for Molecular Physiology ---

2 1

Align Structures at Specific Residues
by Cameron Larson 10 May '22

10 May '22

Hello, I would like to know how to align structures at specific residues. For example, how do I align an ion channel at the selectivity filter instead of aligning the entire structure? Does this ability exist with chimeraX? -Thanks CL

3 2

exporting crosslinks histogram
by Pim J. Huis in t Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15-

1 0

Crossfade just one element
by Rabuck-Gibbons, Jessica 09 May '22

09 May '22

Hello, Would there be a way to apply crossfade ust one part of the model while making a movie? For example, I’m trying to make a movie of several different ligands in one protein. In Chimera, I can show or hide the ligands over a certain number of frames, but this functionality doesn’t seem to exist in ChimeraX. Crossfade is the closest command, but it crossfades the rocking motion as well as the show and hide motion. Is there a way to get around this? Thanks, Jessica [cid2741084884*image001.png(a)01D84823.06CD9060]<https://www.takeda.com/> [cid2741084884*image002.jpg(a)01D84823.06CD9060]<https://www.takeda.com/> Jessica Rabuck-Gibbons Scientist I, Structural Biology Drug Discovery Sciences Takeda Development Center Americas, Inc. (TDCA) 9625 Towne Centre Drive San Diego, CA 92121 USA jessica.rabuck-gibbons(a)takeda.com<mailto:jessica.rabuck-gibbons@takeda.com> The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

2 1

Side by side view in ChimeraX (like pymol grid_mode)
by Thibault TUBIANA 06 May '22

06 May '22

Hello all :-) In ChimeraX, is there a way to display multiple models into the same windows like the "grid_mode" mode in Pymol ? Thank you! Best regards, Thibault Tubiana.

2 2

Chimerax scripting error and passing user supplied arguments
by Ryan Woltz 06 May '22

06 May '22

Dear community, I'm sorry if this is a repeated question, I've seen a few posts about taking in a file for the command line and doing some things then exiting. I got most of this down and I'm sure at this point it is just a matter or correcting a few lines of code. I'm trying to automate a protein modeling protocol and I have 1000 decoys at this point. Now I need to insert the 5 metals into 5 different pockets into all my decoys for a final relax before selecting my top model. I have a template pdb with all the metals in place. For 4 of these metals I have used rosetta align mover to align a decoy onto the template around a single metal binding site, save the pdb, then add on the metal coordinates then repeat for the next binding site. So this method works because the chain is continuous around these metal binding sites. However the final metal binding site is in the center and coordinated by 4 chains coming together and the positioning needs to be very precise. Chimera or chimerax solves this very well but I don't know how to put this into a script. I have a few solutions if someone can help me edit this to work. My script (chimera-data-processing.cxc) looks like this right now. cd results/ open S_0001_X-4-all-chain-A.pdb ###X = 1-1000 open hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb info align #1:240-244,765-769,1290-1294,1815-1819@o to_atoms #2:240-244,765-769,1290-1294,1815-1819@o matchAtomNames true; wait 300 save S_0001_X-4-all-chain-A-sf-aligned.pdb #1 format pdb relModel #2; wait 30 cd ../ close quit This script is perfect if run for have a single model with the exact name written into the script after typing: chimerax-daily --nogui chimera-data-processing.cxc I have two main solutions A) run a while loop that counts down and passes a filename to chimerax: while ( X < 1000 ) chimerax-daily --nogui chimera-data-processing.cxc S_0001_X-4-all-chain-A.pdb hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb Where in the chimerax script I take the arg1 (S_0001*.pdb) and arg2 (hsk2*.pdb)(assuming chimera-data-processing.cxc is arg0) and modify to look like this: open $arg1 open $arg2 ... save $arg1-sf-aligned.pdb #1 format pdb relModel #2; wait 30 Option B is to use the foreach command described in the open command documentation ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html) However, a copy and past of that command: *open myscript.cxc foreach ~/data/*.cif * *or* *open chimera-data-processing.cxc foreach results/S_0001_*-4-* all-chain-A.pdb results in this error: Missing filename suffix foreach I also tried this: chimerax-daily --nogui chimera-data-processing.cxc foreach results/S_0001_*-4-all-chain-A.pdb But it just runs the command. this seems to ignore everything after the first filename. I also read that if I used foreach inside the script I could use $file to replace the filename it is currently working on, would there be a way to fave $file1 and $file2? to automate this I'd also like the change the name of the template file I'm aligning to. I also attempted the python method using sys.arg = arg[1] then running things but I couldn't get it to work because I have no experience in python. What is the suggested way to complete this task? Again this is in a much larger script with user inputs so ideally it would look like this in a script (very shorthanded just for the concepts). I can also run a python command script in my bash sctipt pdb transformations if (y = 5) ###alignment metal number) while ( x < 1000) ###arg0 = command script arg1 = pdb to align arg2 = template pdb with metals chimerax-daily --nogui chimera-command-script.cxc $filenamebase$x-$alignmentnumber-*.pdb $template.pdb ###strings for variables are provided when script is initialized. ###code to extract metal coords for S_0001_$x-4-*.pdb done fi chimera-command-script.cxc: open arg1 open arg2 align model #1 to model #2 on specific atoms save arg1-new-filename.pdb close exit if someone would like a follow-up email with my attempt at chimera python sctipt using runcommand I'm very happy to supply that as a foundation to help fix, I just thought this one is easier to fix since it is really close, the script works but only for 1 pdb at a time. Apologies for bad scripting terminology and confusion with python, I've had to teach coding to myself so I might have misused terms. Thanks for any help that can be given, Ryan

4 6

volume threshold-level
by Dmitry Semchonok 05 May '22

05 May '22

Dear colleagues, Is there a tool in chimeraX that can set the correct volume threshold level when the Molecular weight of the molecule is known? Thank you! Kind regards, Dmitry

3 2

transparency vs. opacity
by Pranav Shah 04 May '22

04 May '22

Hi Elaine, I am trying to control the opacity/transparency of maps..however it seems to me that these two different concepts within the framework although they are used to achieve the same effect... My understanding is that transparency controls the surface being displayed whereas opacity controls the opacity of the color assigned to the surface. Is there room to unify these two concepts in ChimeraX? On an operational level, how do I control the opacity of a color in chimeraX commandline? Currently I am assigning colors based on hexcodes for specific shades... but there isnt a way to take into account the opacity of that shade with hexcodes only... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 1

fitmap
by Dmitry A. Semchonok 04 May '22

04 May '22

2 1

Color by RMSD for nucleic acid
by Rundlet, Emily 03 May '22

03 May '22

Hi ChimeraX developers, Is there a way to color nucleic acids by seq_rmsd? When I use the following, no atoms are colored. mm #1 to #2 matrix Nucleic showAlignment true color byattribute seq_rmsd #2 Thank you in advance for your help! -Emily ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

3 3

security bug in ChimeraX 1.1 and earlier on WIndows
by Greg Couch 03 May '22

03 May '22

FYI, ChimeraX uses the Qt user interface toolkit, and recently a security bug was found in it on Windows. It affects ChimeraX 1.1 and earlier. See https://kb.cert.org/vuls/id/411271 for details. Our recommended fix is to update to the current version of ChimeraX. -- Greg

1 0

Help pages tool hyperlink from Tool index
by William Hofsøy 02 May '22

02 May '22

Hi, I am currently writing some help pages for my tools and noticed that on the Tool index page in the chimerax help pages my tools get listed but not hyperlinked to the pages I write. Is there a way I can fix this? I also noticed that my commands are not listed here. --William

2 1

Dali server alignment
by HONG ZHAN 02 May '22

02 May '22

Dear all, I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. Best, Hong

3 6

Re: [chimerax-users] ChimeraX question
by Tom Goddard 29 Apr '22

29 Apr '22

Hi Ryan, ChimeraX has a "morph" command. Here's an example using it open 2vaa open 2vab matchmaker #2 to #1 morph #1,2 save morph.pdb model #3 allCoordsets true Morphing of course only contains the atoms that are in both structures. So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state. You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures. Tom > On Apr 29, 2022, at 9:28 AM, Kissinger, Ryan (NIH/NIAID) [C] <ryan.kissinger(a)nih.gov> wrote: > > Hi Tom, > > I’m trying to create a morph animation in ChimeraX and I am having a lot of trouble finding decent tutorials online. I have pdb entries for unbound MHC1 and Tapasin and bound MHC1 and Tapasin. If possible I would like to morph between the bound and unbound forms. I would like to do this with ribbon and the atomic models. Any advice? > > Best Regards, > > Ryan

2 1

Re: [chimerax-users] ChimeraX crossfade
by Elaine Meng 28 Apr '22

28 Apr '22

> On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867(a)student.bham.ac.uk> wrote: > > Hi Elaine, > I hope you are well. > I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. > Do you have any advice? > > My code is shown below: > [... edited out by Elaine ...] > > Many thanks, > Daisy > > Sent from Mail for Windows Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively. Unless you are including data that needs to remain private, it is best to send questions to chimerax-users(a)cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.) I'm CC-ing chimerax-users(a)cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private. However, here are some specific notes on the script: (1) the "view 3" command causes an error so I had to comment it out of your script to try it (2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text (3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 2

Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

4 8

Can not save image as tiff format
by 张宁 27 Apr '22

27 Apr '22

Hello ChimeraX group, I want to save the image as tiff format, but it gives me the error "No map chosen to save", could you please help me address this issue? here are two screenshots. Thanks, Ning

3 2

Re: [chimerax-users] [Chimera-users] Questions in ChimeraX comparing with Chimera
by Elaine Meng 27 Apr '22

27 Apr '22

Dear Long Gui, (1) There is no way to open more than one session file in the same instance of ChimeraX, sorry. You can open multiple data files, of course, and have multiple maps, structures, etc. all at the same time, just not from multiple session files. (2) I'm told that the current way to show solid style (also called image style in ChimeraX) planes with zero transparency is to use command volume #2 colormode l8 (the last thing is the letter L except lowercase l and the number 8). See image display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid> Theoretically the following command should also work but currently does not: volume #2 transparency 0 ...although a low almost-zero number should work: volume #2 transparency 0.01 See general display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 27, 2022, at 11:25 AM, Long Gui via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera users, > > I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. > > • How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? > <save.png> > • I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? > <Transparency.png> > > Thanks again and I am very grateful if any advice or help could be provided. > > Long Gui, Ph.D. > Postdoc Researcher, Nicastro Lab > University of Texas Southwestern Medical Center

1 0

Identifying residues based on PAE plot?
by mailman-bounces＠cgl.ucsf.edu 27 Apr '22

27 Apr '22

From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Subject: Identifying residues based on PAE plot? Date: April 27, 2022 at 3:04:30 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Hi everyone, love the "new" work in the dailys for ChimeraX and visualising the PAE and pLDTT scores. As I calculate my AF structures on my own, this helps a lot to analyses the structures. I have one question/suggestion however: If I select a region in the PAE plot, it gets coloured in the the "3D-view", however, I found no way to actually get the residues number or a proper selection for the coloured residues. Is there a way? I'd like to colour multiple selections differently... Another nice feature would be a pLDTT plot, as this enables easier detection of unordered stretches... As always: Many thanks for all the good work! Best Jan -- Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann Institut für Biochemie | University of Cologne Zuelpicher Str. 47 | 50674 Cologne | Germany 📞 +49 (221) 470 3212 📠Fax: +49 (221 470 5066) 📧 jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de> 🌐http://px.uni-koeln.de/ <http://px.uni-koeln.de/> 💎Visit the Cologne Crystallisation facility (C2f) !🌐http://c2f.uni-koeln.de/ <http://c2f.uni-koeln.de/>

2 1

Trouble running ChimeraX 1.3 on Windows 7
by Yu Zhou 27 Apr '22

27 Apr '22

Hi there, I got this error message "api-ms-win-core-path-l1-1-0.dll is missing" when i tried to run ChimeraX 1.3 after installation. My OS is Window 7 and I have no trouble running ChimeraX 1.2.5. I greatly appreciate your help. Yu Zhou

2 1

Unable to restore session: need to update bundle
by Rafael Molina 27 Apr '22

27 Apr '22

Dear ChimeraX staff, I cannot restore a ChimeraX session and ChimeraX suggests to update atomic bundle to version 1.31 or newer (have 1.13.2). When I go to all bundles (https://cxtoolshed.rbvi.ucsf.edu/apps/all <https://cxtoolshed.rbvi.ucsf.edu/apps/all>) I cannot find the way to update it properly. Could you help me to fix the error? Thx ---------------------------------------------------------- Rafael Molina, PhD Dept. Crystallography & Structural Biology. Institute of Physical Chemistry Rocasolano Spanish National Research Council (CSIC) Serrano 119. 28006-Madrid. Spain Phone: +34 91 561 94 00 ext. 961121 E-mail: rmolina(a)iqfr.csic.es <mailto:rmolina@iqfr.csic.es> My Research Gate Profile <https://www.researchgate.net/profile/Rafael-Molina-11> ----------------------------------------------------------

2 1

Re: [chimerax-users] [Chimera-users] Tomogram display
by Elaine Meng 26 Apr '22

26 Apr '22

Hi Shen, If you are asking whether ChimeraX has similar features to Chimera: (1) yes, ChimeraX has a volume viewer tool and "volume" command for density maps, with many of the same options as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> (2) ChimeraX has the same fitting into maps as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> (3) ChimeraX also includes segmentation <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html> (4) similar to Chimera's Volume Tracer, ChimeraX has markers and links and tools for placing them into maps <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> Details between the two programs are not exactly the same, however. There may be some specific thing you need that still requires Chimera, but you can certainly use both programs. To ask questions about ChimeraX specifically, you may wish to use the other mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 26, 2022, at 5:13 AM, Han, Shen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > I want to ask some questions regarding displaying tomogram in ChimeraX. is it possible to reveal the density in the tomogram and trace the objects throughout the tomogram (also docking model in the density) in ChimeraX? > Best wishes, > Shen > _________ > Dr. Shen Han > Postdoctoral Researcher > Max Planck Institute for Multidisciplinary Sciences > Department of Molecular Biology / Cramer Lab > Am Faßberg 11, Göttingen > 37077, Germany

1 0

Re: [chimerax-users] [Chimera-users] Creating Bonds between Models
by Elaine Meng 25 Apr '22

25 Apr '22

Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.…> We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: <https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#…> The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning. By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! > Best regards, > Draven Houser

2 3

Re: [chimerax-users] [Chimera-users] Open Castp file in Chimera X
by Tom Goddard 21 Apr '22

21 Apr '22

Hi Bixia, You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use open ~/Downloads/read_castp.py In other words you have to tell it exactly where the file is unless it is in the directory where you downloaded the file. Also you can use the ChimeraX "cd" command to change to a new current directory in ChimeraX. Best to email this question to the ChimeraX mailing list instead of the Chimera mailing list. Tom > On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Good afternoon, > I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipehttps://rbvi.github.io/chimerax-recipes/castp/castp.html <https://rbvi.github.io/chimerax-recipes/castp/castp.html>. However, when I used the command open <help:user/commands/open.html> read_castp.py, it saidNo such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? > Thank you so much! > Best, > Bixia > > Read CASTP pockets file - ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/castp/castp.html> > We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. > rbvi.github.io <http://rbvi.github.io/> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

2 1

Re: [chimerax-users] palettes and color keys
by Martti Tolvanen 21 Apr '22

21 Apr '22

A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes. Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 12. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 15 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

2 2

ChimeraX command for rmsd color range in angstrom
by Dario Passos 20 Apr '22

20 Apr '22

Dear Chimera community, does anyone know how to add a range of values for the rmsd colors in Chimera X? Something like this (below) in angstrom: => *color byattribute seq_rmsd #1 palette blue:white:red threshold 0:3;6* Thanks, Dario

2 2

Toolshed backend update
by Greg Couch 19 Apr '22

19 Apr '22

FYI, the ChimeraX toolshed will be down this evening (10 p.m PDT, 5 a.m. GMT) to upgrade the back-end. If all goes well, it will be back up within an hour. There should be no user visible changes after the update. However, the back-end change will allow Bundle developers to submit bundles that have commas in the dependencies. -- Greg

1 0

Re: [chimerax-users] Render psuedobonds for RMF models?
by Tom Goddard 19 Apr '22

19 Apr '22

Hi Matthew, Yes. The coarse grain models made from reading RMF files create spheres that are actually atoms, and any atoms can be connected by pseudobonds. I don't know much about RMF in Chimera and ChimeraX. Ben Webb and Conrad Huang worked on that and Conrad retired 2 years ago. It may be that reading RMF creates pseudobonds that are specified in the RMF file. Another way to create pseudobonds is to open a pseudobond file https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> For that you need to figure out the names of the "atoms" (which may represent coarse grain beads) you want to connect. You can open the RMF and hover the mouse over a sphere and a popup will show its name. Also the ChimeraX distance command can create pseudobonds https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html Tom > On Apr 19, 2022, at 8:41 AM, Hancock, Matthew wrote: > > This Message Is From an External Sender > This message came from outside your organization. > > Hi Tom, > > I am a UCSF graduate student in Andrej Sali's group and have a question about Chimera/ChimeraX functionality. I am curious if it is possible to render psuedobonds for multi-scale structures that are read from RMF files. Similar to how it can be done for pdb structures. > > Best > Matthew

1 0

Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

1 0

matchmaker question: restrict moving parts to selection?
by Vorländer,Matthias Kopano 18 Apr '22

18 Apr '22

Hi everyone, Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false". Example: Mm #1:100-200 to #2/100-200 MoveWholeMolecule false This should leave the residues 1-99 in model #1 unchanged. I hope my question is clear. Thanks a lot in advance, Matthias Get Outlook for Android<https://aka.ms/AAb9ysg>

3 4

Saving multiple MRC with derivative names
by Nebojsa Bogdanovic 18 Apr '22

18 Apr '22

Hi, I was looking into the possibility of saving 5 mrc maps after batch z-flipping them. The commands would looks something like this: 1. cd /folder/with/maps 2. open *.mrc 3. volume flip #1-5 4. save [name]*-zflip*.mrc models #6-10 Ideally, the script would save each new (flipped) map as a new .mrc with the suffix "-zflip" or whichever suffix user specifies in the script line 4. Is there such an option if it's implemented? Thank you for the awesome ChimeraX Best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

2 1

0417_1
by 泡沫 17 Apr '22

17 Apr '22

How do you make similar pictures 发自我的iPhone

2 1

Hello
by Brandon Palmer 13 Apr '22

13 Apr '22

My name is brandon palmer I work with Biocryst and came across your software. So far been reading through and I enjoy it's features, and I had a question. Would you happen to have apk version for the use of a Vive 3 Headset? CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

Re: [chimerax-users] [Chimera-users] Chimera X color by attribute middle range value
by Elaine Meng 12 Apr '22

12 Apr '22

Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly. Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0: color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring. By the way, you may be interested in the chimerax-users(a)cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera Community, > > I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. > > Could you please help me figure out how to set attribute range with 3 values as in Chimera? > > Thanks, > Marcell

2 1

Command line disappared
by mhc128＠student.bham.ac.uk 12 Apr '22

12 Apr '22

Hello, I am currently completing a project requiring use of ChimeraX. I'm new to the program, and somehow the command line itself has disappeared for me. I have looked throughout the help section but could not find anything specific on re-enabling the use of the command line. Is there anything I am missing? Thanks for your time.

4 4

Setting the same sdLevel threshold for several volumes
by Moisés Maestro López 11 Apr '22

11 Apr '22

Good morning, I would like to set the threshold of multiple CryoEM Volumes (10-20) at the same time, and I would like to put all of them at the same sdlevel. I use the command: volume #1 sdLevel 2 But this only work for one volume, if I use volume all sdLevel 2, or volume #1 #2 #3 sdLevel 2 It does not work and the threshold are random. In chimera I had a script that I use for doing that but I have not found the way to do it in ChimeraX. In Chimera, I normally called the script with an alias. alias ^allsd runscript ~/chimeraScriptSD.py allsd 3 And the script (chimeraScriptSD.py) was: import sys import chimera from VolumeViewer import Volume mlist = chimera.openModels.list(modelTypes=[Volume]) sdlevel = 2 if len(sys.argv)>1: sdlevel = sys.argv[1] for m in mlist: chimera.runCommand('volume '+str(m)+' sdlevel '+ str(sdlevel)) But I do not know how to do this in ChimeraX. The key point I do not know how to do is to do a loop that say “for any volume in all the opened volumes”. Thanks for your help Moisés

2 4